Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, CB2 1LR, UK.
Am J Bot. 2020 May;107(5):773-789. doi: 10.1002/ajb2.1469. Epub 2020 Apr 29.
Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.
We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework.
Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.
We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.
大型基因组数据集有望解决历史上难以解决的物种关系问题。然而，不同的方法可能会产生相互矛盾的结果，尤其是当进化枝经历了古老而快速的多样化时。在这里，我们分析了石南目植物的古老辐射，并探讨了与物种树推断、基因树信号冲突以及基因和基因组复制推断有关的不确定性来源。
我们使用基于树的同源和同系物检测的层次聚类方法，生成了六个过滤后的基因组数据集，其中包含来自 97 个转录组和基因组的数据。从多个证据来源推断物种关系，包括共享基因复制、基因树冲突、基因边缘分析、串联和基于合并的方法，并在共识框架中进行总结。
我们的共识方法支持与先前研究大致一致的拓扑结构，但表明由于缺乏信息特征、对方法的敏感性以及与古多倍体相关的广泛基因树冲突，数据无法解决几个古老的关系。我们发现了在所有或大多数石南目科辐射之前全基因组复制的证据，并证明树拓扑结构和异速进化率会影响基因组复制的推断位置。
我们提供了关于石南目植物历史的几个假设，并自信地解决了大多数节点，但表明一系列古老的分歧无法用这些数据解决。古多倍体是否是观察到的系统发育冲突的主要来源值得进一步研究。
